"Dr. A Never Met An E. coli That She Didn't Like"

For the great majority of our necropsy cases, we can identify the cause of death right away. There might be a few specifics to sort out, like confirming the specific kind of cancer. But we can usually get most of the diagnosis while on the necropsy floor. 

There are always exceptions. I mentioned in a previous post the handful of cases we were seeing of young dogs with bloody parvo guts that never tested positive for parvovirus. Cultures of tissues from these cases did result in scant to moderate growth of E. coli. Usually, that alone isn't enough to provide a diagnosis.

We culture E. coli and its friends in many of our cases. But not all E. coli are the same. E. coli is everywhere, inside you and outside. It can be considered an environmental contaminant. Animals poop it out, it can live in the soil--you can't get rid of it. But we use sterile techniques to acquire our culture swab samples. So when I get any growth of E. coli, especially from poultry cases, I lean heavily to that as a possible cause of death. 

We've recently had a run of necrotic, hemorrhagic pneumonias in companion animals. Some of them had scant growth of E. coli from lung swabs. But your generic environmental contaminant strain of E. coli doesn't cause that kind of tissue damage. You need a hemolytic strain for this. Our bacteriology group had not been mentioning anything about hemolytic behavior in their reports.

Well. I asked the bacteriology supervisor about this, and it turns out her techs had failed to report the culture results correctly, and the bacteria they cultured were in fact hemolytic. 

I was able to correct the couple of cases that we still had open, but there were half a dozen other cases that were likely hemolytic E. coli infections. But because I've "never met an E. coli that [I] didn't like," according to our pathologist, I had fortunately included a diagnosis of "colibacillosis, suspected" on those cases. 

One of the important aspects of getting a diagnosis is integration. Clinical history, what you see during necropsy, results of tests for viruses and cultures of bacteria, what you see through the microscope when you look at the stained tissue slides, what you learn by reading published literature--all of these disparate types of data get rolled up into a narrative of pathology for each case.

There is one more component of that integration that is much harder to describe. It is a combination of the pathologist's experience, bias, application of the rule that "common diseases present uncommonly" (which means don't go looking for uncommon diseases right off the bat), and a type of gestalt that can develop when you see several similar cases cluster in time (there is definitely a seasonality to some diseases, and some diseases are more common in some species than others). 

The title of this post has complicated subtexts. It is an acknowledgement that I was right in proposing colibacillosis diagnoses for those cases. But it also contains a warning about jumping to diagnostic conclusions without considering all of the differentials. It isn't always E. coli's fault. 

Except when it is.

Lessons From The Past

Early on in the pandemic, I found myself most strongly affected by empty shelves at the grocery store. It was stressful enough to be leaving for work throughout March and April and May when all my neighbors were staying at home. It was stressful to insist back in March that my team at work wear masks when nobody else at the lab was doing so. But seeing large gaps and entire aisles with nothing but stray scraps of paper and dust on the shelves made me the most anxious. Increased my heart rate. I hated going to the store. I stopped my normal weekly trips and stretched out my visits to once every three weeks. 

The weird mass hysteria over toilet paper and paper goods also affected me in an unexpected way. I found myself looking at a paper towel and thinking, well, I've only used this corner of it. I can use it again. And I would carefully set it aside for that purpose.

My grandparents lived through the depression. They are long gone now, but as a kid, I would see them hoard bits of wire and string, re-use a kleenex all day, save tag-ends of soap and cooking grease to accumulate in jars and cans. I distinctly remember thinking at the time that this was odd behavior, but I never really made the connection until now. It's not odd at all when you see those empty store shelves.

I was already thinking a lot about this when I encountered an example of how this pandemic has changed our behavior at work too. 

We use a particular kind of disinfectant to clean the necropsy area at the lab. There are many cleaners that will effectively kill the biological agents that we know are present, but lots of those cleaners are corrosive. We use disinfectant in our boot wash and apply disinfectant solution to many different types of metal, plastic, and ceramic surfaces and tools, and we are ourselves exposed to it. We prefer to use neutral types of disinfectants. 

When we started running low on our stock, we placed an order like we always have. And weeks passed. It wasn't available from that vendor. This vendor might have it, but delivery would be in October or later. Another vendor said, yes, we have it, then the next day said, oops, sorry, no we don't. I started evaluating our options. We could use commercial grade bleach but it really was a choice of last resort. Bleach wasn't available from any vendor either but our bacteriology section had some bottles we could have borrowed. Then our Safety Coordinator came up with a bottle of a very concentrated phenol cleaner that nobody else at the lab wanted to use. Just mixing this stuff up into a solution required full PPE to protect the user. I said, I'll take it! We wear full PPE in necropsy anyway. We could make it work. It wouldn't corrode our boots or our metal tools. If things became dire, we could switch to bleach.

Just a few days later, our shipment of neutral disinfectant arrived. After a brief celebration, I told my team to prepare a purchase requisition for more. The new normal is that we need to order supplies and equipment many weeks in advance. We can no longer wait until we actually need something.

Remember how we started: the pandemic has affected us in subtle ways. I decided that we will reserve our precious neutral disinfectant for important things like tables and equipment. And the phenol cleaner will be used for the boot wash bucket, which is mixed and emptied daily. I told my two technicians, both in their late 20s/early 30s, about my grandparents and the Great Depression, but I am sure they didn't understand how that related to using phenol cleaner for the boot wash.

Hoarding. Choosing less desirable items to preserve things we have decided are more desirable. Using less. Not odd behavior at all.